Genomic DNA detection method and system thereof

Abstract

A method to directly detect eukaryotic or prokaryotic genomic DNA is disclosed. The invention relates to a method for printing, immobilizing, hybridizing and directly detecting a target nucleic acid sequence in a sample of methylated genomic DNA. Additionally, this invention provides a system for the detection of a target nucleic acid sequence including a flat substrate to bind methylated DNA in discrete patterns and a plurality of labeled target binding probes specific for a target nucleic acid sequence.

We claim:  
     
         1 . A method for detecting a target nucleic acid sequence comprising: 
 (a) applying a plurality of samples of methylated DNA on to a flat substrate to form discrete patterns of said methylated DNA onto said flat substrate;    (b) hybridizing said plurality samples of methylated DNA with labeled target binding probes specific for a target nucleic acid sequence;    (c) detecting the label of said labeled target binding probes; and    (d) associating said label with said target nucleic acid sequence.    
     
     
         2 . The method of  claim 1  wherein said discrete patterns are 50 to 10,000 microns in diameter.  
     
     
         3 . The method of  claim 1  wherein said plurality of samples of methylated DNA is immobilized on said substrate.  
     
     
         4 . The method of  claim 1  wherein said substrate is functionalized with a chemical selected from the group consisting of: aldehyde, amine, carboxyl, polylysine, silanated, silyated, epoxy and nitrocellulose.  
     
     
         5 . The method of  claim 1  wherein said methylated DNA is genomic DNA.  
     
     
         6 . The method of  claim 1  wherein said methylated DNA is a subset of genomic DNA.  
     
     
         7 . The method of  claim 1  wherein said methylated DNA is sonicated to form subsets of genomic DNA.  
     
     
         8 . The method of  claim 1  wherein the said flat substrate is a glass slide.  
     
     
         9 . A system for the detection of a target nucleic acid sequence comprising: 
 (a) a flat substrate to bind methylated DNA in discrete patterns; and    (b) a plurality of labeled target binding probes specific for a target nucleic acid sequence.    
     
     
         10 . The system of  claim 9  wherein said discrete patterns are 50 to 10,000 microns in diameter.  
     
     
         11 . The system of  claim 9  wherein said substrate is functionalized with a chemical selected from the group consisting of: aldehyde, amine, carboxyl, polylysine, silanated, silyated, epoxy and nitrocellulose.  
     
     
         12 . The system of  claim 9  wherein said methylated DNA is genomic DNA.  
     
     
         13 . The system of  claim 9  wherein said methylated DNA is a subset of genomic DNA.  
     
     
         14 . The system of  claim 9  wherein said methylated DNA is sonicated to form subsets of genomic DNA.  
     
     
         15 . The system of  claim 9  wherein the said flat substrate is a glass slide.  
     
     
         16 . The method of  claim 9  wherein said system further includes a plurality of labeled target binding probes specific for a control sequence of DNA.  
     
     
         17 . The method of  claim 1  wherein said methylated DNA is selected from the group consisting of: mitochondrial DNA, chloroplastic DNA and DNA/RNA hybrids.